Parenting: Elementary Ages Community

My husbands 9 year old daughter has just recently been visiting us. I do not know if he is used to her behavior or if he is just as frustrated as I am. I am kind of afraid to talk to him about it, because I do not want to put out the impression that I do not like his daughter to come visit us.
My husband is ten years older then me and has a 12 year old son and his 9 year old daughter from two different relationships. We get his son every other weekend he lives kind of far away or we might see him more often. His son is such a good kid! I have never seen him shed a tear or get upset!
His daughter was molested by her step dad, which I dont know much about cause it happened before I was around, and its not my place to talk about. But her mother has not allowed my husband to see his daughter for over a year until recently. She doesnt live far away at all either, just across town, so we could have her every day if she wanted to see us.

I am so confused by her behavior, because my husband would call and call and call to talk to her and her mom would always tell him his daughter didnt want to see or talk to him. Then one day his daughter started calling him, and asked if he would come visit her at her aunts house. We went to see her, and she hid from her dad in a closet when we got to her aunts house.
Neither of us really understand why she was afraid of him, we assume it was because she was molested and was having trust issues with men. Hes a really good dad and is very patient with her. I can tell it hurt his feelings when his daughter wasnt talking to him, but he was patient and she finally came around.

My pet Rabbit scratched her on Saturday after I warned her not to carry him around the yard or hed get scared and scratch her. It was a very small scratch that didnt even break the skin, and she was screaming I WANT MY MOMMY and wouldnt tell me what happened. I knew what happened because her big brother told me, and he was rolling his eyes and calling her a cry baby. I was very patient and washed her arm off with a cold rag and pretended that I was the rabbits voice and told her that the rabbit was sorry. She pouted with the wet rag on her arm for an hour and a half, and was still whimpering. And then like magic she jumped up and wanted to go to the park to play soccer.
Later that night she started crying in the car because we were on our way home from the grocery store and we were talking about MAYBE going to the haunted house. All we did was ask her if shed like to go or if it would be too scary and she burst into tears I DONT WANNA GO! NOOOOooo! just screaming again and bawling!
Later that night before bed she started crying and wanted her mom to come get her because she was scared. That I can understand, sleeping in a strange house is scary.
But the next day she called her dad just BAWLING I can hear her squeaking "please daddy come and get me I miss you" Which is really cute that she misses him, but why all the crying???
She went home and a few hours later she called just bawling and squealing you can barely understand her, "Daddy can I come over tomoro and see you?" And my husband is telling her yes sweet heart of course you can why are you crying so much, why are you so upset? Then her mom gets on the phone and her mom says she doesnt know why she is crying either.
I am just concerned about her, I dont know why just about anything makes her burst into tears at the drop of a hat. I am not sure how we can correct this if at all, or to be patient and wait it out? I have never encountered a child her age crying so much over things she will not even explain.... And Im new to this mom thing.
Thanks experienced moms!